Receptor
PDB id Resolution Class Description Source Keywords
1I6L 1.72 Å EC: 6.1.1.2 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRN SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP GEOBACILLUS STEAROTHERMOPHILUS CLASS I TRNA SYNTHETASE AARS INDUCED FIT TRPRS LIGASE
Ref.: HIGH-RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANY SYNTHETASE (TRPRS) COMPLEXED WITH TRYPTOPHANYL-5'AM ACTA CRYSTALLOGR.,SECT.D V. 57 1595 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:370;
A:371;
A:372;
A:373;
A:374;
A:375;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NH4 A:400;
Invalid;
none;
submit data
18.038 H4 N [NH4+...
SO4 A:360;
A:361;
A:362;
A:363;
A:364;
A:365;
A:366;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
TYM A:350;
Valid;
none;
submit data
533.431 C21 H24 N7 O8 P c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DK4 1.9 Å EC: 6.1.1.2 CRYSTAL STRUCTURE ANALYSIS OF TRYPTOPHANYL-TRNA SYNTHETASE F BACILLUS STEAROTHERMOPHILUS IN COMPLEX WITH INDOLMYCIN AND GEOBACILLUS STEAROTHERMOPHILUS AARS INHIBITOR LIGASE-LIGASE INHIBITOR COMPLEX
Ref.: SELECTIVE INHIBITION OF BACTERIAL TRYPTOPHANYL-TRNA SYNTHETASES BY INDOLMYCIN IS MECHANISM-BASED. J.BIOL.CHEM. V. 291 255 2016
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1I6K - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 1MAU - CIT C6 H8 O7 C(C(=O)O)C....
3 1M83 Kd = 0.4 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1I6M - TYM C21 H24 N7 O8 P c1ccc2c(c1....
5 5DK4 Ki = 2 nM 5BX C14 H15 N3 O2 C[C@H](c1c....
6 1I6L - TYM C21 H24 N7 O8 P c1ccc2c(c1....
7 2OV4 Ki = 2 mM AQP C10 H17 N5 O16 P4 c1nc(c2c(n....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1I6K - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 1MAU - CIT C6 H8 O7 C(C(=O)O)C....
3 1M83 Kd = 0.4 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1I6M - TYM C21 H24 N7 O8 P c1ccc2c(c1....
5 5DK4 Ki = 2 nM 5BX C14 H15 N3 O2 C[C@H](c1c....
6 1I6L - TYM C21 H24 N7 O8 P c1ccc2c(c1....
7 2OV4 Ki = 2 mM AQP C10 H17 N5 O16 P4 c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1I6K - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 1MAU - CIT C6 H8 O7 C(C(=O)O)C....
3 1M83 Kd = 0.4 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1I6M - TYM C21 H24 N7 O8 P c1ccc2c(c1....
5 5DK4 Ki = 2 nM 5BX C14 H15 N3 O2 C[C@H](c1c....
6 1I6L - TYM C21 H24 N7 O8 P c1ccc2c(c1....
7 2OV4 Ki = 2 mM AQP C10 H17 N5 O16 P4 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TYM; Similar ligands found: 244
No: Ligand ECFP6 Tc MDL keys Tc
1 TYM 1 1
2 FA5 0.72381 1
3 SRP 0.7 0.972973
4 YAP 0.691589 0.986486
5 AMO 0.673077 0.972973
6 LAD 0.669811 0.923077
7 WSA 0.666667 0.845238
8 5AL 0.663366 0.945946
9 ME8 0.648148 0.9
10 NB8 0.648148 0.935065
11 8QN 0.632075 0.945946
12 PAJ 0.626168 0.875
13 CA0 0.62 0.933333
14 4AD 0.611111 0.96
15 DLL 0.605505 0.972603
16 PTJ 0.603604 0.886076
17 OOB 0.601852 0.972603
18 YLP 0.59322 0.878049
19 A2D 0.585859 0.932432
20 3UK 0.585586 0.959459
21 WAQ 0.580357 0.922078
22 B5V 0.580357 0.946667
23 YLB 0.578512 0.878049
24 YLC 0.578512 0.9
25 AN2 0.578431 0.894737
26 AHX 0.576577 0.910256
27 BA3 0.574257 0.932432
28 AYB 0.572581 0.86747
29 AP5 0.568627 0.932432
30 B4P 0.568627 0.932432
31 ADP 0.568627 0.906667
32 YLA 0.564516 0.878049
33 AT4 0.563107 0.871795
34 00A 0.5625 0.922078
35 AR6 0.561905 0.932432
36 PRX 0.561905 0.858974
37 APR 0.561905 0.932432
38 1ZZ 0.561404 0.853659
39 FYA 0.561404 0.945946
40 ANP 0.560748 0.883117
41 B5M 0.560345 0.934211
42 ADX 0.557692 0.819277
43 M33 0.557692 0.894737
44 AD9 0.556604 0.883117
45 AMP 0.555556 0.905405
46 XAH 0.555556 0.876543
47 A 0.555556 0.905405
48 PR8 0.552632 0.911392
49 HEJ 0.552381 0.906667
50 ATP 0.552381 0.906667
51 ACP 0.552381 0.907895
52 50T 0.552381 0.87013
53 9SN 0.551724 0.910256
54 TXA 0.547826 0.921053
55 5FA 0.54717 0.906667
56 AQP 0.54717 0.906667
57 B5Y 0.547009 0.934211
58 SAP 0.542056 0.860759
59 AGS 0.542056 0.860759
60 YLY 0.541985 0.86747
61 A1R 0.539823 0.897436
62 ABM 0.539216 0.881579
63 3OD 0.534483 0.933333
64 ACQ 0.53211 0.907895
65 9ZA 0.530973 0.897436
66 25A 0.530973 0.932432
67 9ZD 0.530973 0.897436
68 N0B 0.529851 0.901235
69 AP2 0.528846 0.896104
70 A12 0.528846 0.896104
71 AU1 0.528302 0.883117
72 4UV 0.525 0.934211
73 V1N 0.525 0.932432
74 DQV 0.52459 0.945946
75 ATF 0.522523 0.871795
76 A22 0.522124 0.92
77 DAL AMP 0.522124 0.92
78 LAQ 0.520325 0.853659
79 SRA 0.519608 0.858974
80 GAP 0.518182 0.907895
81 6YZ 0.517857 0.907895
82 OAD 0.517241 0.933333
83 ADV 0.513761 0.921053
84 RBY 0.513761 0.921053
85 A3R 0.513043 0.897436
86 TXE 0.507937 0.897436
87 M24 0.507463 0.8875
88 SON 0.504673 0.946667
89 APC 0.504587 0.896104
90 TAT 0.504505 0.871795
91 T99 0.504505 0.871795
92 5SV 0.504348 0.817073
93 9X8 0.504274 0.884615
94 25L 0.504202 0.92
95 4UU 0.504065 0.934211
96 BT5 0.5 0.86747
97 ADQ 0.5 0.933333
98 NAI 0.5 0.897436
99 DND 0.5 0.946667
100 NXX 0.5 0.946667
101 4UW 0.5 0.898734
102 TYR AMP 0.5 0.96
103 80F 0.496241 0.901235
104 IOT 0.496124 0.86747
105 7MD 0.491935 0.9
106 NAX 0.488189 0.911392
107 TXD 0.488189 0.897436
108 AMP DBH 0.487805 0.883117
109 ADP PO3 0.486486 0.905405
110 G3A 0.483871 0.886076
111 BIS 0.483333 0.85
112 MAP 0.482759 0.860759
113 ADP ALF 0.482456 0.8375
114 ALF ADP 0.482456 0.8375
115 T5A 0.480916 0.878049
116 48N 0.480315 0.910256
117 G5P 0.48 0.886076
118 VO4 ADP 0.478261 0.894737
119 ADP VO4 0.478261 0.894737
120 SSA 0.478261 0.813953
121 6V0 0.476562 0.886076
122 LSS 0.474576 0.795455
123 F2R 0.473684 0.878049
124 NAE 0.471014 0.909091
125 NAD 0.470149 0.945946
126 TSB 0.470085 0.790698
127 5CA 0.470085 0.813953
128 A5A 0.469565 0.8
129 AP0 0.469231 0.8625
130 ARG AMP 0.468254 0.865854
131 AFH 0.468254 0.898734
132 GA7 0.468254 0.896104
133 YSA 0.467742 0.835294
134 NAQ 0.467626 0.886076
135 MYR AMP 0.467213 0.831325
136 LMS 0.466667 0.797619
137 CNA 0.466165 0.946667
138 BV8 0.465517 0.811111
139 GTA 0.464567 0.853659
140 A3D 0.463235 0.933333
141 KAA 0.46281 0.786517
142 A A 0.46281 0.906667
143 DSZ 0.462185 0.835294
144 54H 0.461538 0.781609
145 VMS 0.461538 0.781609
146 AF3 ADP 3PG 0.461538 0.875
147 OMR 0.461538 0.843373
148 BVT 0.460227 0.802198
149 PAP 0.460177 0.893333
150 COD 0.459259 0.825581
151 139 0.458647 0.8875
152 ADJ 0.458647 0.865854
153 UPA 0.458015 0.897436
154 AOC 0.457944 0.789474
155 53H 0.457627 0.772727
156 ADP BMA 0.454545 0.907895
157 UP5 0.453846 0.909091
158 2A5 0.451327 0.858974
159 GSU 0.45082 0.835294
160 BJW 0.45 0.820225
161 52H 0.449153 0.772727
162 RAB 0.44898 0.786667
163 ADN 0.44898 0.786667
164 XYA 0.44898 0.786667
165 AMP NAD 0.448529 0.945946
166 BTX 0.448529 0.855422
167 PPS 0.448276 0.797619
168 8PZ 0.448 0.835294
169 ATP A A A 0.448 0.918919
170 EAD 0.447552 0.8875
171 9K8 0.447154 0.747253
172 JB6 0.447154 0.897436
173 7MC 0.44697 0.878049
174 4TC 0.44697 0.910256
175 A3P 0.445455 0.905405
176 DZD 0.445255 0.898734
177 A4P 0.443609 0.835294
178 G5A 0.443478 0.813953
179 5X8 0.442478 0.826667
180 TAD 0.44186 0.875
181 5AS 0.441441 0.752809
182 NSS 0.438017 0.813953
183 0WD 0.437956 0.886076
184 A2R 0.436975 0.92
185 5CD 0.435644 0.773333
186 COT 0.435583 0.818182
187 NDE 0.435374 0.921053
188 P1H 0.435374 0.865854
189 LPA AMP 0.435115 0.831325
190 SA8 0.434783 0.765432
191 ATR 0.434783 0.88
192 NVA LMS 0.434426 0.786517
193 AR6 AR6 0.434109 0.932432
194 ZID 0.433566 0.933333
195 8X1 0.433333 0.786517
196 SAI 0.431034 0.794872
197 SAH 0.431034 0.805195
198 LEU LMS 0.430894 0.786517
199 CA3 0.430303 0.818182
200 SFG 0.429825 0.813333
201 SMM 0.428571 0.741176
202 NAJ PZO 0.428571 0.8625
203 AHZ 0.427481 0.831325
204 P5A 0.427419 0.777778
205 SAM 0.42735 0.746988
206 5N5 0.425743 0.763158
207 7D5 0.424528 0.820513
208 EEM 0.423729 0.746988
209 7D3 0.423423 0.822785
210 A4D 0.421569 0.763158
211 7D4 0.421053 0.822785
212 A2P 0.419643 0.891892
213 DTA 0.419048 0.779221
214 G A A A 0.417266 0.8625
215 4TA 0.417266 0.865854
216 3AM 0.416667 0.866667
217 V3L 0.415254 0.932432
218 6AD 0.411765 0.829268
219 ARU 0.41129 0.785714
220 NDC 0.410596 0.886076
221 FB0 0.410596 0.797753
222 A5D 0.410256 0.779221
223 NJP 0.410072 0.909091
224 EP4 0.409524 0.725
225 6RE 0.409091 0.753086
226 4YB 0.409091 0.837209
227 ITT 0.408696 0.855263
228 3DH 0.407407 0.74359
229 A G 0.407143 0.873418
230 NAJ PYZ 0.406897 0.821429
231 NDP 0.405797 0.886076
232 M2T 0.40566 0.707317
233 DCA 0.405594 0.816092
234 FDA 0.405229 0.825581
235 FNK 0.405063 0.818182
236 S7M 0.404959 0.746988
237 7C5 0.40458 0.833333
238 U A G G 0.404255 0.873418
239 67D 0.402878 0.795455
240 MTA 0.401869 0.74359
241 IMO 0.401786 0.866667
242 J7C 0.401786 0.7625
243 62X 0.4 0.72093
244 A3S 0.4 0.826667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DK4; Ligand: 5BX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5dk4.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5DK4; Ligand: 5BX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5dk4.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5DK4; Ligand: ATP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5dk4.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5DK4; Ligand: ATP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5dk4.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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